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15
votes
23
replies
2.0k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
5 weeks ago • updated 8 days ago
Chris
• 0
14
votes
17
replies
1.2k
views
Why p value inconsistent when using different number of pathway score?
limma
18 days ago • updated 7 days ago
Chris
• 0
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 19 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 20 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
8
votes
23
replies
957
views
Convert Seurat Object to Summarised Experiment or ExpressionSet
SummarizedExperiment
ExpressionSet
updated 27 days ago by
Robert Castelo
★ 3.3k • written 28 days ago by
Bine
▴ 40
8
votes
7
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 2 days ago by
Sara
• 0 • written 6.7 years ago by
Sylvain Foisy
▴ 80
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 8 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
6
votes
5
replies
446
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
written 9 weeks ago by
Kim
• 0
6
votes
12
replies
4.9k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 16 days ago
shepherl
3.9k
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 19 days ago by
i.atanasoai
• 0 • written 15 months ago by
mohammedtoufiq91
▴ 10
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 24 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 180
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 15 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 6 days ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
5
votes
6
replies
433
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 25 days ago by
ATpoint
★ 4.1k • written 29 days ago by
nhaus
▴ 30
5
votes
9
replies
1.3k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 20 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
9
replies
934
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
27 days ago • updated 20 days ago
Chris
• 0
4
votes
2
replies
549
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
6 days ago • updated 2 days ago
gene_bioconductor
▴ 10
4
votes
9
replies
436
views
Memory errors using read.bismark?
dmrseq
bsseq
27 days ago • updated 1 day ago
Juan Higareda
• 0
4
votes
6
replies
440
views
FilterByExpr low counts with small sample size
edgeR
21 days ago • updated 16 days ago
Jonathan
▴ 10
3
votes
6
replies
281
views
Surrogate variable analysis for paired RNA seq experiment
RUVSeq
sva
27 days ago
nhaus
▴ 30
3
votes
0
replies
91
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
7 days ago
shepherl
3.9k
3
votes
3
replies
231
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 15 days ago by
Michael Love
42k • written 16 days ago by
WardDeb
• 0
3
votes
4
replies
293
views
Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it does not happen in Linux
GenomAutomorphism
updated 8 hours ago by
Mike Smith
★ 6.5k • written 3 days ago by
robersy
• 0
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by
Michael Love
42k • written 15 days ago by
i.sudbery
▴ 40
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 17 hours ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
3
votes
18
replies
2.9k
views
News:
List of Deprecated Packages for Bioc3.18
Deprecation
devel
Bioconductor
Devel
10 months ago • updated 21 days ago
shepherl
3.9k
3
votes
3
replies
346
views
permutation test in edgeR
rna-seq
edgeR
updated 17 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Netanel
• 0
3
votes
4
replies
225
views
Help with error using camera() in limma
CAMERA
limma
8 days ago
Chris
• 0
3
votes
3
replies
215
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
26 days ago • updated 20 days ago
jacques.imbert
• 0
3
votes
1
reply
180
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 19 days ago by
Gordon Smyth
50k • written 20 days ago by
Shaimaa Gamal
• 0
3
votes
2
replies
219
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 16 days ago by
Guido Hooiveld
★ 3.9k • written 18 days ago by
fernanda.backsouza
▴ 10
3
votes
1
reply
1.5k
views
Job:
Post Doctoral position in AI (Deep learning / Machine learning) approaches for Cancer Research, MRC Cancer Unit, University of Cambridge, UK
job
Job
machine learning
deep learning
computational biology
written 6.3 years ago by
Shamith.Samarajiwa
▴ 180
3
votes
4
replies
206
views
Method to find pathways different between 2 groups
fgsea
GSVA
CAMERA
updated 21 hours ago by
Gordon Smyth
50k • written 2 days ago by
Chris
• 0
3
votes
1
reply
87
views
How to save the DEXSeq results
DEXSeq
updated 2 days ago by
Michael Love
42k • written 2 days ago by
Sara
• 0
3
votes
3
replies
241
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
bioinf
▴ 10
3
votes
5
replies
184
views
Help with running egsea()
EGSEA
2 days ago • updated 17 hours ago
Chris
• 0
3
votes
1
reply
756
views
News:
[Pre-print] Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
biorxiv
spatialLIBD
News
written 4.2 years ago by
Leonardo Collado Torres
★ 1.0k
2
votes
2
replies
193
views
OrgDb for maize
clusterProfiler
OrgDb
biomaRt
Zea_mays
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
sansan
• 0
2
votes
13
replies
434
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
17 days ago • updated 14 days ago
fernanda.backsouza
▴ 10
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 21 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
2
replies
176
views
ComplexHeatmap: change the names of a HeatmapAnnotation object
ComplexHeatmap
26 days ago • updated 23 days ago
daniel.carbajo
• 0
2
votes
5
replies
276
views
get BM error
ensembldb
updated 14 days ago by
James W. MacDonald
65k • written 14 days ago by
Fara
• 0
2
votes
3
replies
177
views
package goseq seems to be not available on the latest version of R
goseq
updated 2 days ago by
Gordon Smyth
50k • written 5 days ago by
Patrycja
▴ 20
2
votes
2
replies
199
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
26 days ago • updated 25 days ago
julia_mcdonough
• 0
2
votes
2
replies
392
views
[Diffbind] Blacklist error: Error: Invalid Normalization and Unable to apply Blacklist/Greylist
DiffBind
Normalization
27 days ago • updated 26 days ago
Henry
▴ 10
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 8 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
2
votes
9
replies
397
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Alexandre
• 0
2
votes
2
replies
172
views
[DiffBind] Obtaining normalization factors
DiffBind
26 days ago • updated 22 days ago
Henry
▴ 10
2
votes
3
replies
329
views
ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with variable number of continuous columns
ComplexHeatmap
23 days ago • updated 22 days ago
daniel.carbajo
• 0
2
votes
5
replies
248
views
How to retrieve gene ontology GO class from gene list?
GO.db
goTools
updated 13 days ago by
James W. MacDonald
65k • written 14 days ago by
bandconductor
• 0
200 results • Page
1 of 4
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Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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